I'm trying to use pbs to queue jobs in our cluster. So I modified my job_conf.xml file to reflect 'pbs' queuing. Here is my job_conf.xml
<job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" worker="10"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="batch"> <destination id="batch" runner="pbs"/> <destination id="big_jobs" runner="pbs"> <param id="Resource_List">walltime=72:00:00</param> </destination> </destinations>
When I start the galaxy server, I get an error below:
. . AssertionError: The Python pbs-python package is required to use this feature, please install it or correct the following error: ImportError /hpcdata/galaxy/.venv/lib/python2.7/site-packages/pbs/_pbs.so: undefined symbol: pbs_submit_hash_ext
Documentation on WIki suggests to modify eggs.ini file but running, ./scripts/check_eggs.py indicates that eggs have been replaced with wheels. So I'm not sure if that is an issue.
I have already set the path for $DRMAA_LIBRARY_PATH as /usr/lib64/libdrm.so.2 (again there is no libdrmaa.so as indicated in wiki)
Also, the pythons version is as below python --version Python 2.7.5